RIck I think there are a set of compromises that you bring up in your dialogue of limitations. I think having a fixed and we can nominate as the aft end of the boat is quite probably the most worthy solution. The question of location is a far more difficult one.

Certainly if there are two engines then thrust can be used to manoeuvre in close quarters, but Im hard pressed on having two engines, it is more expensive not only in engines but all aspects of control. There is also a temptation in having 2 rather underpowered engines as is the case with twin engine aircraft, for which pilots say if you lose an engine the surviving engine just takes you to the crash site. Statistically greater chance of losing an engine where there are two.

So, a single more powerful engine with the capacity to rotate in its well? Im yet to see any workable examples but I wouldnt give up the hope that it cant be done. The benefit to two engines then is that you do not need to have augmented thrust, with one however you probably do. Its not impossible to do this with retractable deflectors, rather like the engine thrust reversers on the back of jets.

Finally the location, there are two very obvious choices, it is either on the aft beam closest to the hull, or within a well aft of the aft cabin. Clearly lowering the engine from a well has some virtues, but it is putting a hole in the hull, and on this hull where there are no other holes or apertures it seems a damn of a thing to do.

I was interested in what you were describing the location of the trough, I would have thought a bow wave forward rescinding into a trough that begins to dissipate aft of half way along the hull where the following wave begins to propagate. That might have made the aft beam location a reasonable choice?